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Abstract The adjustment of a gravel bed during cycles of sediment storage was analyzed for a flume experiment, designed to study the effects of episodic sediment supply regimes. As the bed aggraded and degraded due to changes in sediment feed, it developed a complex topography with bedforms at different scales (e.g., pebble-clusters, bars). Sediment inputs increased bedload rates and promoted large changes in bed morphology. Without an external supply, the bed armored, which increased bed stability, counteracted bed degradation, and decreased bedload rates. Fully-mobile gravel (2–8 mm) was the only fraction that exhibited a deficit over the experiment. Preferential storage of coarse grains caused the development of a sediment wedge upstream and downstream fining on the bed surface. The storage of sand was also significant (60 % of feed) probably because of infiltration (e.g., in the upstream wedge) and hiding effects promoted by bed armor and structures. Size-selective transport caused a cumulative increase in bed slope, which was likely to affect sediment transport capacity. The large variability in bedload rates for same levels of bed storage indicated that sediment availability and bed state were the main controls on sediment transport regime. We provide empirical evidence that cycles of aggradation and degradation, caused by changes in sediment feed upstream, condition bed composition and topography, and the rate and texture of sediment output. Highlights • Aggradation-degradation cycles condition sediment transport rates. • Partial mobility promotes coarse sediment storage upstream and downstream fining. • Sand storage is significant within lag coarse deposits. • Differences in sediment availability cause hysteresis in bedload rates. [ABSTRACT FROM AUTHOR]